# HG changeset patch
# User cschu
# Date 1466975064 14400
# Node ID b3cd759a00645cd771a630852a95fa130d5775fd
# Parent a297bbcd1c01c7c45a236b59114cd29e673a2016
Uploaded
diff -r a297bbcd1c01 -r b3cd759a0064 data_manager/featurecounts_gxfloader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/featurecounts_gxfloader.xml Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,28 @@
+
+
+ GFF/GTF loader
+
+ featurecounts
+ FCOUNT_SCRIPT_PATH
+
+
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diff -r a297bbcd1c01 -r b3cd759a0064 data_manager/make_json.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/make_json.py Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,33 @@
+import json
+import argparse
+import os
+import shutil
+
+
+
+parser = argparse.ArgumentParser(description='Create data manager json.')
+parser.add_argument('--dbkey', action='store')
+parser.add_argument('--provider', action='store')
+parser.add_argument('--ref', action='store')
+parser.add_argument('--out', action='store')
+
+args = parser.parse_args()
+
+def main(args):
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.dbkey.lower()
+ data_manager_entry['name'] = args.dbkey
+ data_manager_entry['path'] = '.'
+ data_manager_entry['ref'] = args.ref
+ data_manager_entry['provider'] = args.provider
+ data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry))
+ params = json.loads(open(args.out).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.join(os.getcwd(), 'featurecount_gxf')
+ for filename in os.listdir(output_path):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
+
+if __name__ == '__main__':
+ main(args)
diff -r a297bbcd1c01 -r b3cd759a0064 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,21 @@
+
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diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/data_manager/featurecounts_gxfloader.xml
--- a/gffdm/data_manager/featurecounts_gxfloader.xml Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-
-
- GFF/GTF loader
-
- featurecounts
- FCOUNT_SCRIPT_PATH
-
-
-
-
-
-
-
-
-
-
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diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/data_manager/make_json.py
--- a/gffdm/data_manager/make_json.py Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-import json
-import argparse
-import os
-import shutil
-
-
-
-parser = argparse.ArgumentParser(description='Create data manager json.')
-parser.add_argument('--dbkey', action='store')
-parser.add_argument('--provider', action='store')
-parser.add_argument('--ref', action='store')
-parser.add_argument('--out', action='store')
-
-args = parser.parse_args()
-
-def main(args):
- data_manager_entry = {}
- data_manager_entry['value'] = args.dbkey.lower()
- data_manager_entry['name'] = args.dbkey
- data_manager_entry['path'] = '.'
- data_manager_entry['ref'] = args.ref
- data_manager_entry['provider'] = args.provider
- data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry))
- params = json.loads(open(args.out).read())
- target_directory = params['output_data'][0]['extra_files_path']
- os.mkdir(target_directory)
- output_path = os.path.join(os.getcwd(), 'featurecount_gxf')
- for filename in os.listdir(output_path):
- shutil.move(os.path.join(output_path, filename), target_directory)
- file(args.output, 'w').write(json.dumps(data_manager_json))
-
-if __name__ == '__main__':
- main(args)
diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/data_manager_conf.xml
--- a/gffdm/data_manager_conf.xml Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-
-
-
-
-
-
-
-
diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/tool-data/gene_sets.loc.sample
--- a/gffdm/tool-data/gene_sets.loc.sample Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools
-# to use gene/exon annotations in the GFF/GTF format. You will need
-# to add all the gene set annotations in this configuration file.
-# Because of this file, galaxy tools are able to access gene annotations
-# provided as GFF / GTF files by selecting on:
-# - Priorty (defined by the order in the file)
-# - Provider
-# - dbkey (reference genome id)
-#
-# The gene_sets.loc file syntax is:
-#
-# *optional
-#
-# Please ensure maximally one TAB (\t) between two columns!
-# ---------------------------------------------------------
-#
-# In case you have TWO or MORE providers PER dbkey, the one mentioned
-# first in the file, should have the "default" priority.
-#
-
-
-
-# [UCSC - UCSC Genes: knownGene]
-
-#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/
-#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/
-
-
-
-# [RefSeq Genes: RefGene]
-# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
-
-
-
-# [ Ensembl]
-# link: http://www.ensembl.org/info/data/ftp/index.html
-
-#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
-#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/tool_data_table_conf.xml.sample
--- a/gffdm/tool_data_table_conf.xml.sample Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-
-
-
-
- value, dbkey, path, provider, ref
-
-
-
diff -r a297bbcd1c01 -r b3cd759a0064 gffdm/tool_dependencies.xml
--- a/gffdm/tool_dependencies.xml Sun Jun 26 16:58:34 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-
- $REPOSITORY_INSTALL_DIR
-
-
-
-
-
diff -r a297bbcd1c01 -r b3cd759a0064 tool-data/gene_sets.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_sets.loc.sample Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,39 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use gene/exon annotations in the GFF/GTF format. You will need
+# to add all the gene set annotations in this configuration file.
+# Because of this file, galaxy tools are able to access gene annotations
+# provided as GFF / GTF files by selecting on:
+# - Priorty (defined by the order in the file)
+# - Provider
+# - dbkey (reference genome id)
+#
+# The gene_sets.loc file syntax is:
+#
+# *optional
+#
+# Please ensure maximally one TAB (\t) between two columns!
+# ---------------------------------------------------------
+#
+# In case you have TWO or MORE providers PER dbkey, the one mentioned
+# first in the file, should have the "default" priority.
+#
+
+
+
+# [UCSC - UCSC Genes: knownGene]
+
+#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/
+#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/
+
+
+
+# [RefSeq Genes: RefGene]
+# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
+
+
+
+# [ Ensembl]
+# link: http://www.ensembl.org/info/data/ftp/index.html
+
+#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
+#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
diff -r a297bbcd1c01 -r b3cd759a0064 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, path, provider, ref
+
+
+
diff -r a297bbcd1c01 -r b3cd759a0064 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,9 @@
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+
+